Government says 60 victims now confirmed dead and number of people affected soars to 2.44 million, mostly around Manila.

Thousands more Philippine flood survivors have crammed into evacuation centres as waist-high water covered vast farming regions and the death toll from a week of misery rose to 60.

The flooding that submerged 80 per cent of Manila early in the week had largely subsided, allowing people to return to their homes on Friday, but vital rice-growing areas to the north remained submerged as more rain fell there.

"We need something to eat. I haven't gone to work or been paid for a week," said Rogelio Soco, a construction worker and father of three children in the small farming town of Apalit, about 60km from Manila.

Soco, 60, said the floods, which began on Monday, were the worst the area had seen since a huge typhoon struck in the early 1970s, and other locals also said they had not experienced anything like it for decades.

Around Apalit, formerly green rice paddies had been turned into an enormous inland ocean of brown water.

Some people stood waist-deep in water and fished in the rice fields as rain continued to fall, while others hitched rides from town to town on government-provided flat-bed trucks.

Nearly two weeks of monsoon rains across the Philippines' main island of Luzon peaked with a 48-hour deluge earlier this week that battered Manila and surrounding regions.

The government's disaster co-ordination council said Friday that 60 people had been confirmed killed in this week's floods, triple the number on Thursday.

The extra deaths occurred mainly in the provinces during the initial deluges from Monday to Wednesday, but government officials in the outlying areas could not immediately report the casualties to Manila headquarters, the council said.

"A lot of them have just reported now because their first priority was response [to the floods]," Anna Orallo, the council's deputy administrator, told the AFP news agency.

The number of people now confirmed killed across the country since the rains first began in late July is 113, according to the council's data.

Struggling to cope

Meanwhile, the government said it was struggling to cope with the scale of a relief effort across Luzon that was expected to last for weeks.

Tens of thousands of people were continuing to stream into evacuation centres that were already overcrowded and unable to provide enough immediate relief goods.

"The water is still high and the local government units are getting overwhelmed," Social Welfare Secretary Corazon Soliman said, referring to the farming provinces north of Manila where she was touring on Friday.

"We have evacuation centres that are congested. That is the whole problem."

Just over 362,000 people were sheltering in evacuation centres on Friday, nearly 50,000 more than on Thursday, according to the disaster council.

The number of people officially affected by the floods also rose to 2.44 million, from 2.1 million on Thursday.

In Manila, clean-up operations were under way in riverside communities that endured waters up to two metres high on Tuesday and Wednesday.

The Southeast Asian archipelago endures about 20 major storms or typhoons each rainy season, many of which are deadly.

But this week's rains were the worst to hit Manila since Tropical Storm Ketsana killed 464 people in 2009.

Ramon Paje, the environment secretary, warned that the Philippines must prepare for more intense rains caused by climate change, describing the latest deluge as the "new normal".